Transportation from Naples to Syracuse in July

Palermo is on the other side of the island. Are you planning to travel around Sicily? If not, fly into Catania and take the bus to Siracusa. If you haven't booked accommodations in Siracusa, try to find a place in Ortigia, the old part of town.

The night train will not be fun, because at Villa San Giovanni the train will be uncoupled, loaded onto a ferry, unloaded, and recoupled. I doubt that you will be able to sleep through it.

I booked a berth in a cuchetta (obviously not the same as trying for a private compartment) not long before leaving for Sicily last June. I was headed to Catania. I assume that was the same train you'd be taking. I can tell you that the ride was pretty miserable because the train jerked to the left and right constantly. It wasn't the steady up-and-down bumping I remembered from the night trains I took decades ago. I believe the issue was that the speed of the train--though not particularly fast--was too much for the current condition of the tracks. I suggest Googling to see whether you can find other people's opinions on that night train. I guess it's possible that the somewhat more comfortable beds in the sleeping compartments would help a bit with the jerky ride.

There was another problem with my trip--about a 3-hour delay just before or after the crossing to Sicily. They were doing track work. It didn't look short-term. You might be able to find out whether that's still going on.

I'd seriously consider flying this route, or the overnight Palermo ferry if its schedule coincides with yours. I'm not sure how the pricing will work out; since you'll want a cabin, I suspect the flight would be cheaper.

If you do end up landing in Palermo, you'll have an opportunity to take the train across the interior of the island. Most likely there are buses along that route as well, but I haven't checked. The interior is very interesting, and if you have time, you might want to stop over in Enna to see some of the interior sights.

Buses from Catania to Siracusa are readily available since you will be arriving on Monday. Sunday would be more of a challenge. There's also train service, possibly less frequent. In both cities the bus and train stations are fairly close together. In Catania, though, there are different offices for different bus lines. Get as much info as you can online before you arrive, and expect it to take a bit of time to get to the right office and to find your bus. A lot (most?) of the inter-city buses from Catania make a stop at the Catania airport, so you probably will have no difficulty getting into town via public bus if you want to. Again, I'm assuming we're talking about Monday here, not Sunday.

Patience !!!!

.....the timetable is updated on the 2nd Sunday in June. There is no way to tell if that's what's happening,.....

That is exactly what is happening. But there will be little change from period to period. If you want to see the schedule, look on the same day of the week, next week or next month

I would fly Naples to Catania. that's what we did - we did the train too, and unless you have some special reason for wanting to take a very long train ride, honestly there are better ways to spend your vacation hours. We flew into Catania and then took the bus that takes you to Siracusa/Ortigia. easy peasy. Check EasyJet.

I can't imagine a night train in the south of Italy in the summer -- that sounds like sheer misery. Flying may not be as romantic, but in reality will be much better for this part of your trip.

Check EasyJet NOW, because people have already been buying tickets for the summer, I imagine.